New York Times COVID-19 data visualization

Loading required package: lattice
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======================
Welcome to d3heatmap version 0.9.0

Type citation('d3heatmap') for how to cite the package.
Type ?d3heatmap for the main documentation.

The github page is: https://github.com/talgalili/d3heatmap/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/d3heatmap/issues
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     https://stackoverflow.com/questions/tagged/d3heatmap
======================


Attaching package: ‘d3heatmap’

The following objects are masked from ‘package:base’:

    print, save


Attaching package: ‘lubridate’

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Introduction

The purpose of this notebook is to give data locations, data ingestion code, and code for rudimentary analysis and visualization of COVID-19 data provided by New York Times, [NYT1].

The following steps are taken:

• Ingest data

  • Take COVID-19 data from The New York Times, based on reports from state and local health agencies, [NYT1].

  • Take USA counties records data (FIPS codes, geo-coordinates, populations), [WRI1].

• Merge the data.

• Make data summaries and related plots.

• Make corresponding geo-plots.

• Do “out of the box” time series forecast.

• Analyze fluctuations around time series trends.

Note that other, older repositories with COVID-19 data exist, like, [JH1, VK1].

Remark: The time series section is done for illustration purposes only. The forecasts there should not be taken seriously.

Preliminary defintions

From the help of tolower:

capwords <- function(s, strict = FALSE) {
    cap <- function(s) paste(toupper(substring(s, 1, 1)),
                  {s <- substring(s, 2); if(strict) tolower(s) else s},
                             sep = "", collapse = " " )
    sapply(strsplit(s,  split = " "), cap, USE.NAMES = !is.null(names(s)))
}

Import data

NYTimes USA states data

if( !exists("dfNYDataStates") ) {
  dfNYDataStates <- read.csv( "https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv", 
                              colClasses = c("character", "character", "character", "integer", "integer"), 
                              stringsAsFactors = FALSE )
  colnames(dfNYDataStates) <- capwords(colnames(dfNYDataStates))
}
head(dfNYDataStates)

dfNYDataStates$DateObject <- as.POSIXct(dfNYDataStates$Date)

summary(as.data.frame(unclass(dfNYDataStates), stringsAsFactors = TRUE))

         Date                 State            Fips           Cases             Deaths        DateObject                 
 2020-03-28:   55   Washington   :  578   53     :  578   Min.   :      1   Min.   :    0   Min.   :2020-01-21 00:00:00  
 2020-03-29:   55   Illinois     :  575   17     :  575   1st Qu.:  14840   1st Qu.:  326   1st Qu.:2020-07-14 00:00:00  
 2020-03-30:   55   California   :  574   06     :  574   Median : 104087   Median : 1967   Median :2020-11-25 00:00:00  
 2020-03-31:   55   Arizona      :  573   04     :  573   Mean   : 301818   Mean   : 5868   Mean   :2020-11-25 03:46:21  
 2020-04-01:   55   Massachusetts:  567   25     :  567   3rd Qu.: 375902   3rd Qu.: 7044   3rd Qu.:2021-04-08 00:00:00  
 2020-04-02:   55   Wisconsin    :  563   55     :  563   Max.   :4303611   Max.   :65020   Max.   :2021-08-20 00:00:00  
 (Other)   :29164   (Other)      :26064   (Other):26064                                                                  

Summary by state:

by( data = as.data.frame(unclass(dfNYDataStates)), INDICES = dfNYDataStates$State, FUN = summary )

Alternative summary:

Hmisc::describe(dfNYDataStates)

NYTimes USA counties data

if(!exists("dfNYDataCounties") ) {
  dfNYDataCounties <- read.csv( "https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-counties.csv", 
                                colClasses = c("character", "character", "character", "character", "integer", "integer"),
                                stringsAsFactors = FALSE )
  colnames(dfNYDataCounties) <- capwords(colnames(dfNYDataCounties))
}
head(dfNYDataCounties)

dfNYDataCounties$DateObject <- as.POSIXct(dfNYDataCounties$Date)

summary(as.data.frame(unclass(dfNYDataCounties), stringsAsFactors = TRUE))

         Date                County             State              Fips             Cases             Deaths          DateObject                 
 2021-04-05:   3250   Washington:  15969   Texas   : 125930          :  14884   Min.   :      0   Min.   :    0.0   Min.   :2020-01-21 00:00:00  
 2021-08-03:   3250   Unknown   :  13405   Georgia :  82329   53061  :    578   1st Qu.:    150   1st Qu.:    2.0   1st Qu.:2020-08-07 00:00:00  
 2021-08-04:   3250   Jefferson :  13375   Virginia:  67742   17031  :    575   Median :    888   Median :   17.0   Median :2020-12-11 00:00:00  
 2021-08-10:   3250   Franklin  :  12807   Kentucky:  60652   06059  :    574   Mean   :   5435   Mean   :  108.1   Mean   :2020-12-10 08:46:17  
 2021-08-20:   3250   Jackson   :  12183   Missouri:  58478   04013  :    573   3rd Qu.:   3118   3rd Qu.:   61.0   3rd Qu.:2021-04-16 00:00:00  
 2021-04-07:   3249   Lincoln   :  12145   Illinois:  52104   06037  :    573   Max.   :1377253   Max.   :33694.0   Max.   :2021-08-20 00:00:00  
 (Other)   :1618432   (Other)   :1558047   (Other) :1190696   (Other):1620174                     NA's   :36857                                  

US county records

if(!exists("dfUSACountyData")){
  dfUSACountyData <- read.csv( "https://raw.githubusercontent.com/antononcube/SystemModeling/master/Data/dfUSACountyRecords.csv", 
                               colClasses = c("character", "character", "character", "character", "integer", "numeric", "numeric"),
                               stringsAsFactors = FALSE )
}
head(dfUSACountyData)

summary(as.data.frame(unclass(dfUSACountyData), stringsAsFactors = TRUE))

         Country          State                   County          FIPS        Population            Lat             Lon         
 UnitedStates:3143   Texas   : 254   WashingtonCounty:  30   01001  :   1   Min.   :      89   Min.   :19.60   Min.   :-166.90  
                     Georgia : 159   JeffersonCounty :  25   01003  :   1   1st Qu.:   10980   1st Qu.:34.70   1st Qu.: -98.23  
                     Virginia: 134   FranklinCounty  :  24   01005  :   1   Median :   25690   Median :38.37   Median : -90.40  
                     Kentucky: 120   JacksonCounty   :  23   01007  :   1   Mean   :  102248   Mean   :38.46   Mean   : -92.28  
                     Missouri: 115   LincolnCounty   :  23   01009  :   1   3rd Qu.:   67507   3rd Qu.:41.81   3rd Qu.: -83.43  
                     Kansas  : 105   MadisonCounty   :  19   01011  :   1   Max.   :10170292   Max.   :69.30   Max.   : -67.63  
                     (Other) :2256   (Other)         :2999   (Other):3137                                                       

Merge data

dsNYDataCountiesExtended <- 
  dfNYDataCounties %>% 
  dplyr::inner_join( dfUSACountyData %>% dplyr::select_at( .vars = c("FIPS", "Lat", "Lon", "Population") ), by = c( "Fips" = "FIPS" ) )
dsNYDataCountiesExtended

Basic data analysis

ParetoPlotForColumns( as.data.frame(lapply(dsNYDataCountiesExtended[,c("Cases", "Deaths")], as.numeric)), c("Cases", "Deaths"), scales = "free" )

Geo-histogram

ggplot2

Note that in the plots in this sub-section we filter out Hawaii and Alaska.

ggplot2::ggplot(dsNYDataCountiesExtended[ dsNYDataCountiesExtended$Lon > -130, c("Lat", "Lon", "Cases")]) +
  ggplot2::geom_point( ggplot2::aes(x = Lon, y = Lat, fill = log10(Cases)), alpha = 0.01, size = 0.5, color = "blue" ) + 
  ggplot2::coord_quickmap()

Leaflet

The most recent versions of leaflet RStudio are having problems with the visualization below.

cf <- colorBin( palette = "Reds", domain = log10(dsNYDataCountiesExtended$Cases), bins = 10 )

m <- 
  leaflet( dsNYDataCountiesExtended[, c("Lat", "Lon", "Cases")] ) %>%
  addTiles() %>% 
  addCircleMarkers( ~Lon, ~Lat, radius = ~ log10(Cases), fillColor = ~ cf(log10(Cases)), color = ~ cf(log10(Cases)), fillOpacity = 0.8, stroke = FALSE, popup = ~Cases )
m

dsNYDataCountiesExtended

Heat-map plots

An alternative of the geo-visualization is to use a heat-map plot.

Cases

Make a heat-map plot by sorting the rows of the cross-tabulation matrix (that correspond to states):

matSDC <- xtabs( Cases ~ State + Date, dfNYDataStates, sparse = TRUE)
d3heatmap::d3heatmap( log10(matSDC+1), cellnote = as.matrix(matSDC), scale = "none", dendrogram = "row", colors = "Blues") #, theme = "dark")

Warning in RColorBrewer::brewer.pal(n, pal) :
  n too large, allowed maximum for palette RdYlBu is 11
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(n, pal) :
  n too large, allowed maximum for palette RdYlBu is 11
Returning the palette you asked for with that many colors

Deaths

Cross-tabulate states with dates over deaths and plot:

matSDD <- xtabs( Deaths ~ State + Date, dfNYDataStates, sparse = TRUE)
d3heatmap::d3heatmap( log10(matSDD+1), cellnote = as.matrix(matSDD), scale = "none", dendrogram = "row", colors = "Blues") #, theme = "dark")

Warning in RColorBrewer::brewer.pal(n, pal) :
  n too large, allowed maximum for palette RdYlBu is 11
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(n, pal) :
  n too large, allowed maximum for palette RdYlBu is 11
Returning the palette you asked for with that many colors

Time series analysis

In this section we do simple “forecasting” (not a serious attempt).

Make time series data frame in long form:

dfQuery <- 
  dfNYDataStates %>% 
  dplyr::group_by( Date, DateObject ) %>% 
  dplyr::summarise_at( .vars = c("Cases", "Deaths"), .funs = sum )
dfQueryLongForm <- tidyr::pivot_longer( dfQuery, cols = c("Cases", "Deaths"), names_to = "Variable", values_to = "Value")
head(dfQueryLongForm)

Plot the time series:

ggplot(dfQueryLongForm) +
  geom_line( aes( x = DateObject, y = log10(Value) ) ) +
  facet_wrap( ~Variable, ncol = 1 )

Cases

Fit using ARIMA:

fit <- forecast::auto.arima( dfQuery$Cases )
fit

Series: dfQuery$Cases 
ARIMA(5,2,2) 

Coefficients:
          ar1      ar2      ar3      ar4      ar5      ma1     ma2
      -0.0709  -0.7032  -0.4278  -0.3593  -0.5618  -0.6517  0.6317
s.e.   0.0615   0.0445   0.0462   0.0332   0.0428   0.0773  0.0363

sigma^2 estimated as 302286721:  log likelihood=-6439.15
AIC=12894.3   AICc=12894.55   BIC=12929.15

Plot “forecast”:

plot( forecast::forecast(fit, h = 20) )
grid(nx = NULL, ny = NULL, col = "lightgray", lty = "dotted")

Deaths

Fit with ARIMA:

fit <- forecast::auto.arima( dfQuery$Deaths )
fit

Series: dfQuery$Deaths 
ARIMA(3,2,2) 

Coefficients:
         ar1      ar2      ar3      ma1     ma2
      0.9997  -0.6314  -0.1766  -1.3792  0.6554
s.e.  0.0562   0.0606   0.0527   0.0440  0.0351

sigma^2 estimated as 140488:  log likelihood=-4229.64
AIC=8471.28   AICc=8471.43   BIC=8497.42

Plot “forecast”:

plot( forecast::forecast(fit, h = 20) )
grid(nx = NULL, ny = NULL, col = "lightgray", lty = "dotted")

Fluctuations

We want to see does the time series data have fluctuations around its trends and estimate the distributions of those fluctuations. (Knowing those distributions some further studies can be done.)

This can be efficiently using the software monad QRMon, [AAp2, AA1]. Here we load the QRMon package:

#devtools::install_github(repo = "antononcube/QRMon-R")
library(QRMon)

Warning: replacing previous import ‘magrittr::set_names’ by ‘purrr::set_names’ when loading ‘QRMon’

Fluctuations presence

Here we plot the consecutive differences of the cases and deaths:

dfQueryLongForm <- 
  dfQueryLongForm %>% 
  dplyr::group_by( Variable ) %>% 
  dplyr::arrange( DateObject ) %>% 
  dplyr::mutate( Difference = c(0, diff(Value) ) ) %>% 
  dplyr::ungroup()
ggplot(dfQueryLongForm) +
  geom_line( aes( x = DateObject, y = Difference ) ) +
  facet_wrap( ~Variable, ncol = 1, scales = "free_y" )

From the plots we see that time series are not monotonically increasing, and there are non-trivial fluctuations in the data.

Absolute and relative errors distributions

Here we take interesting part of the cases data:

dfQueryLongForm2 <- 
  dfQueryLongForm %>% 
  dplyr::filter( difftime( DateObject, as.POSIXct("2020-05-01")) >= 0 ) %>% 
  dplyr::mutate( Regressor = as.numeric(DateObject, origin = "1900-01-01") )

Here we specify a QRMon workflow that rescales the data, fits a B-spline curve to get the trend, and finds the absolute and relative errors (residuals, fluctuations) around that trend:

qrObj <- 
  QRMonUnit(dfQueryLongForm2 %>% dplyr::filter( Variable == "Cases") %>% dplyr::select( Regressor, Value) ) %>% 
  QRMonRescale(regressorAxisQ = F, valueAxisQ = T) %>% 
  QRMonEchoDataSummary %>% 
  QRMonQuantileRegression( df = 16, probabilities = 0.5 )

$Dimensions
[1] 477   2

$Summary
   Regressor             Value       
 Min.   :1.588e+09   Min.   :0.0000  
 1st Qu.:1.599e+09   1st Qu.:0.1319  
 Median :1.609e+09   Median :0.4842  
 Mean   :1.609e+09   Mean   :0.4791  
 3rd Qu.:1.619e+09   3rd Qu.:0.8454  
 Max.   :1.629e+09   Max.   :1.0000  

Here we plot the fit:

qrObj <- qrObj %>% QRMonPlot(datePlotQ = T)

Here we plot absolute errors:

qrObj <- qrObj %>% QRMonErrorsPlot(relativeErrorsQ = F, datePlotQ = T)

Here is the summary:

summary( (qrObj %>% QRMonErrors(relativeErrorsQ = F) %>% QRMonTakeValue)[[1]]$Error )

      Min.    1st Qu.     Median       Mean    3rd Qu.       Max. 
-0.0035826 -0.0006384  0.0000000  0.0002062  0.0006325  0.0102965 

Here we plot relative errors:

qrObj <- qrObj %>% QRMonErrorsPlot(relativeErrorsQ = T, datePlotQ = T)

Here is the summary:

summary( (qrObj %>% QRMonErrors(relativeErrorsQ = T) %>% QRMonTakeValue)[[1]]$Error )

      Min.    1st Qu.     Median       Mean    3rd Qu.       Max. 
-0.6406639 -0.0018016  0.0000000 -0.0009474  0.0019173  0.0536856 

Refereces

[NYT1] The New York Times, Coronavirus (Covid-19) Data in the United States, (2020), GitHub.

[WRI1] Wolfram Research Inc., USA county records, (2020), System Modeling at GitHub.

[JH1] CSSE at Johns Hopkins University, COVID-19, (2020), GitHub.

[VK1] Vitaliy Kaurov, Resources For Novel Coronavirus COVID-19, (2020), community.wolfram.com.

[AA1] Anton Antonov, “A monad for Quantile Regression workflows”, (2018), at MathematicaForPrediction WordPress.

[AAp1] Anton Antonov, Heatmap plot Mathematica package, (2018), MathematicaForPrediciton at GitHub.

[AAp2] Anton Antonov, Monadic Quantile Regression Mathematica package, (2018), MathematicaForPrediciton at GitHub.